<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix #VERSION# documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>

<body>

<table class=nav>
  <tr>
    <td><a href="index.html"><img src="../left.png"></a></td>
    <td><a href="../index.html"><img src="../home.png"></a></td>
    <th>The MRtrix configuration file</th>
    <td><a href="mrtrix.html"><img src="../right.png"></a></td>
  </tr>
</table>

<h2><a name="location">Location</a></h2>
<p>
MRtrix applications will attempt to read configuration information 
from a number of possible locations, if they exist. 
There will in general be a system-wide configuration file, 
and a user specific configuration file.
Their exact location is platform-dependent, as detailed below:
</p>
<table class=desc>
  <tr><th>platform</th><th>location</th></tr>
  <tr><td>Unix</td><td>system: <kbd>/etc/mrtrix.conf</kbd><br>user: <kbd>$HOME/.mrtrix.conf</kbd></td></tr>
  <tr><td>Windows</td><td>system: <kbd>C:\mrtrix.conf</kbd><br>user: <kbd>$HOME\mrtrix.conf</kbd> (e.g. <kbd>C:\Documents and Settings\username\mrtrix.conf</kbd>)</td></tr>
</table>

<p>
The system-wide configuration file will be read first (if found),
followed by the user configuration file (if found).
In case of conflict between the system-wide and user configuration,
the user settings will be used.
If a particular configuration parameter is not defined, 
MRtrix will use hard-coded defaults.
</p>


<p class=sep><a href="#top">top</a></p>
<h2><a name="format">Format</a></h2>
<p>
The configuration files are text files, with each line containing a key: value pair.
For example:
</p>
<pre>
Analyse.LeftToRight: false
NumberOfThreads: 2
</pre>
<p>
<strong>Note:</strong> key names are case-sensitive.
</p>
<p>
The value entry may be interpreted by MRtrix applications as either:
<ul>
  <li>Boolean: allowed values here are <kbd>true</kbd> or <kbd>false</kbd></li>
  <li>Integer: any integer value</li>
  <li>Floating-point: any floating-point value</li>
  <li>Text: any text string, without any further interpretation</li>
</ul>



<p class=sep><a href="#top">top</a></p>
<h2><a name="list">List of parameters</a></h2>
<p>
These parameters are currently interpreted by MRtrix:
</p>
<table class=args>
  <tr><td>Analyse.LeftToRight</td><td>bool</td><td>specifies the order in which voxels are stored in Analyse format image data files.</td></tr>
  <tr><td>NumberOfThreads</td><td>integer</td><td>number of threads to lauch in multi-threaded applications (e.g. <a href='../commands/csdeconv.html'>csdeconv</a>)</td></tr>
</table>



<table class=nav>
  <tr>
    <td><a href="index.html"><img src="../left.png"></a></td>
    <td><a href="index.html"><img src="../up.png"></a></td>
    <td><a href="../index.html"><img src="../home.png"></a></td>
    <th><a href='#top'>top</a></th>
    <td><a href="mrtrix.html"><img src="../right.png"></a></td>
  </tr>
</table>

<p class=footer>
Donald Tournier<br>
MRtrix version #VERSION#<br>
Last updated #MTIME#
</p>


</body>
</html>
